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PARIS — The European Union on Friday formally published new guidelines explicitly banning any EU funding of and cooperation with Israeli institutions operating in territories beyond the pre-1967 lines, amid vigorous Israeli objections.

The new directive, to take effect at the start of 2014, requires the EU and its members to cease any joint activity or funding with Israeli entities working over the Green Line in the West Bank and Jerusalem, and in the Golan Heights.

The measure also require any future agreements between Israel and the EU to include a clause in which Israel accepts the European Union’s position that all territory over the Green Line does not belong to Israel — a requirement that is anathema to Israel.

The restrictions are ostensibly meant to help Israel, by ensuring that it remains a recipient of EU funds, provided that the money doesn’t cross the Green Line, the EU has said. But officials in Jerusalem have said the measures will also serve to alienate Israel, and predetermine its future borders.

The EU holds that Jewish settlements in territories such as the West Bank and east Jerusalem are illegal. The Palestinians claim those territories for their hoped-for state.

After EU officials announced plans this week for the new guidelines, Israeli Prime Minister Benjamin Netanyahu spoke with several European leaders to express his opposition and seek to have the regulations amended or delayed — to no avail.

EU foreign policy chief Catherine Ashton said the document released Friday “is meant to clarify the EU’s position” and is not meant to harm efforts toward Mideast peace. Very little EU funding currently goes to Israeli bodies in the territories, but there are concerns in Israel that implementation of the directives could impact Israeli entities with even marginal connections over the Green Line.

On Thursday, sources in the EU told Army Radio that the EU was prepared to engage in negotiations with Israel to amend the implementation of the restrictions.

Netanyahu spent the last several days holding marathon talks with European diplomats and leaders over the measure, reportedly telling them that the timing could harm the chances for restarting peace talks with the Palestinians. President Shimon Peres also sought to intervene.

Sandra de Waele, the deputy EU ambassador to Israel, said Tuesday that the measure was designed to ensure that EU financial support “not benefit [Israeli] entities” beyond the Green Line, because it was the EU’s position that such entities were illegal. She said there had been concern that these entities had indeed been benefiting from EU funds. She stressed that the directive would not affect private businesses.

A Jerusalem official told Maariv in response to the restrictions’ publication that “the Europeans have a right to do whatever they like with their money. However, their directives also influence what Israeli institutions do with funds that do not come from the EU, and that is unacceptable.”